Duplicate records after CalculateGenotypePosteriors

Hi,

I follow this thread to execute results from a trio but I discover there are many duplicate records after CalculateGenotypePosteriors.

Code brief describe here:
java -Xmx16g -jar gatk-package-4.0.0.0-local.jar CalculateGenotypePosteriors -R Homo_sapiens_assembly38.fasta -ped trio.ped -supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.gz -V trio.recal.vcf.gz -O trio.recal.refine.vcf.gz
I also discover the output is not gz format, just vcf.

Recalibrated variants (part)

chr1    3872413 .       AG      A       400.09  PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum        GT:AD:DP:GQ:PL  0/0:27,0:27:81:0,81,712 0/0:45,0:45:99:0,111,1665   0/1:17,21:38:99:440,0,469
chr1    3872414 .       GA      G       29.18   PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD       GT:AD:DP:GQ:PL  0/0:29,0:29:16:0,16,666 0/1:48,10:58:69:69,0,1051       0/0:35,3:38:54:0,54,912
chr1    3883678 .       A       G       2352.16 PASS    AC=2;AF=0.333;AN=6;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=311;ExcessHet=3.9794;FS=1.518;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.164e+00;SOR=0.709;VQSLOD=23.18;culprit=MQ      GT:AD:DP:GQ:PL  0/0:59,0:59:99:0,120,1800       0/1:69,51:120:99:964,0,1565 0/1:65,67:132:99:1420,0,1292

After CalculateGenotypePosteriors (part)

chr1    3872413 .       AG      A       400.09  PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;PG=0,0,0;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum       GT:AD:DP:GQ:JL:JP:PL:PP 0/0:27,0:27:81:80:80:0,81,712:0,81,772      0/0:45,0:45:99:80:80:0,111,1665:0,111,1725      0/1:17,21:38:99:80:80:440,0,469:440,0,529
chr1    3872414 .       GA      G       29.18   PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;PG=0,0,0;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD      GT:AD:DP:GQ:JL:JP:PL:PP 0/0:29,0:29:16:16:16:0,16,666:0,16,719  0/1:48,10:58:69:16:16:69,0,1051:69,0,1067   0/0:35,3:38:54:16:16:0,54,912:0,54,928
chr1    3872413 .       AG      A       400.09  PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;PG=0,0,0;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum       GT:AD:DP:GQ:JL:JP:PL:PP 0/0:27,0:27:81:80:80:0,81,712:0,81,772      0/0:45,0:45:99:80:80:0,111,1665:0,111,1725      0/1:17,21:38:99:80:80:440,0,469:440,0,529
chr1    3872414 .       GA      G       29.18   PASS    AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;PG=0,0,0;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD      GT:AD:DP:GQ:JL:JP:PL:PP 0/0:29,0:29:16:16:16:0,16,666:0,16,719  0/1:48,10:58:69:16:16:69,0,1051:69,0,1067   0/0:35,3:38:54:16:16:0,54,912:0,54,928
chr1    3883678 .       A       G       2352.16 PASS    AC=2;AF=0.333;AN=6;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=311;ExcessHet=3.9794;FS=1.518;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;PG=0,0,6;POSITIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.164e+00;SOR=0.709;VQSLOD=23.18;culprit=MQ     GT:AD:DP:GQ:JL:JP:PL:PP 0/0:59,0:59:99:119:119:0,120,1800:0,120,1805        0/1:69,51:120:99:119:119:964,0,1565:964,0,1631  0/1:65,67:132:99:119:119:1420,0,1292:1420,0,1358

Issue · Github
by Sheila

Issue Number
4346
State
closed
Last Updated
Closed By
lbergelson

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